Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 128.97 kDa 
• Atom Count: 9125 
• Residue Count: 1119 
• Unique protein chains: 3

2WHB

Truncation and Optimisation of Peptide Inhibitors of CDK2, Cyclin A Through Structure Guided Design

• DOI: 10.2210/pdb2WHB/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-03 Released: 2009-06-09 
• Deposition Author(s): Kontopidis, G., Andrews, M.J., McInnes, C., Plater, A., Innes, L., Renachowski, S., Cowan, A., Fischer, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.264 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Literature

Truncation and optimisation of peptide inhibitors of cyclin-dependent kinase 2-cyclin a through structure-guided design.

Kontopidis, G., Andrews, M.J., McInnes, C., Plater, A., Innes, L., Renachowski, S., Cowan, A., Fischer, P.M.

(2009) ChemMedChem 4: 1120-1128

• PubMed: 19472269 
• DOI: 10.1002/cmdc.200900093
• Primary Citation of Related Structures:  
  2WEV, 2WFY, 2WHB


• PubMed Abstract: 
  

Peptides that inhibit cyclin-dependent kinase 2 by blocking the macromolecular substrate recruitment site of cyclin A were simplified, for example, by replacement of dipeptide units with beta-amino acids. The smallest inhibitor retaining activity was a tripeptide, whose binding mode was confirmed by X-ray crystallography. This result suggests that nonpeptidic cyclin groove inhibitors may be feasible therapeutic agents.The cyclin-dependent kinase 2-cyclin A complex is an important regulator of the DNA-synthesis phase of the mammalian cell cycle, which is frequently deregulated in cancer. Rather than blocking the ATP-binding site of the apparently redundant kinase subunit, targeting the binding site for macromolecular substrates and regulatory proteins of cyclin A represents a promising strategy to enforce tumour-selective apoptosis. The cyclin-binding groove can be blocked with comparatively small synthetic peptides, which indirectly leads to inhibition of kinase function, but these peptides are metabolically labile and membrane impermeable. As part of our ongoing effort to develop more druglike peptidomimetics derived from cyclin-groove-binding peptides, we report the results of our studies aimed at a detailed understanding of the structural determinants required for effective binding. Using a combination of peptide synthesis, biochemical assays and X-ray crystallography, we show that it is possible to simplify peptide structures through the replacement of dipeptide units in which one of the residues is not directly involved in binding, through the introduction of beta-amino acid residues that retain only the dipeptide residue side chain that is important for binding. This approach also allowed us to probe spatial constraints in general, as well as the importance of peptide backbone hydrogen-bonding functions. Our identification of potent beta-homoleucine-containing tetrapeptide inhibitors, as well as the finding that an optimised N-terminally acetylated tripeptide retains some cyclin A-binding affinity, suggest that the pharmacological targeting of the cyclin A binding groove may be feasible.

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Organizational Affiliation: 

Veterinary School, University of Thessaly, Karditsa 43100, Greece.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION PROTEIN KINASE 2	A, C	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS  P24941 GTEx  ENSG00000123374

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIN-A2	B, D	260	Homo sapiens	Mutation(s): 0  Gene Names: CCNA2, CCN1, CCNA
Find proteins for P20248 (Homo sapiens) Explore P20248  Go to UniProtKB:  P20248
NIH Common Fund Data Resources
PHAROS  P20248 GTEx  ENSG00000145386

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ARG-ARG-L3O-PFF	E, F	5	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
L3O	E,F	L-PEPTIDE LINKING	C7 H15 N O3		LEU
PFF	E,F	L-PEPTIDE LINKING	C9 H10 F N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.264 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.423	α = 90
b = 114.924	β = 90
c = 154.468	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-05-03 
• Released Date: 2009-06-09 
Deposition Author(s): Kontopidis, G., Andrews, M.J., McInnes, C., Plater, A., Innes, L., Renachowski, S., Cowan, A., Fischer, P.M.

Revision History 

• Version 1.0: 2009-06-09
  Type: Initial release
  
• Version 1.1: 2011-08-24
  Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
• Version 1.2: 2017-02-08
  Changes: Source and taxonomy
• Version 2.0: 2019-04-24
  Changes: Data collection, Database references, Derived calculations, Other, Polymer sequence